Are there any tools that can automatically generate properly formatted citations (from bare URLs?) Bare links on Wikipedia are supposed to be replaced with properly citations. Are there any tools or software to make this easier?

It works with the following newspapers:
BBC, Daily Mail, Daily Mirror, The Daily Telegraph, Huffington Post, Huffington Post Canada, The New York Times, The Washington Post, The Boston Globe, The Times of India, Financial Times, The Economist, Wall Street Journal, Business Week, Ars Technica, TG Daily

The problem (for me) is that I have to teach the script how to handle each website. Another problem the newspapers change their formatting of their pages sometimes, and then I have to update the script. If there would be a W3C standard for presenting the four required fields: title, date of publication, names of the authors and name of the publication, then the script would be much shorter, won't require updates and it would work with any publication that implements the standard.

Wikipedia itself has a limited number of citation helpers. On your Preferences page, Gadgets tab, set "Citation expander", which is described here. Then when you are editing a page, there will be a "Cite" toggle which will show a toolbar where you can choose a template, such as "cite web" for a basic url reference. There is also support for automatically filling in info given a DOI or some other IDs.

Reflinks (click the "interactive" tab) is an external took that completes bare references already present in the article. It attempts to automatically fill in fields such as title and publisher by taking them from the webpage. However, the tool is not perfect, and you should inspect each reference and fix any inaccurate or missing fields.